AD	Alzheimer’s disease
ALT	Alanine aminotransferase
AMPs	Antimicrobial proteins
ANGPTL4	Angiopoietin-like protein 4
APC	Antigen-presenting cell
ARG	Antibiotic resistance genes
ASD	Autism spectrum disorder
AST	Aspartate aminotransferase
ASC	Acute severe colitis
BCFAs	Branched-chain fatty acids
BHB	Beta (β) hydroxybutyrate
CD	Crohn’s Disease
CKD	Chronic kidney disease
CLA	Conjugated linoleic acid
CVD	Cardiovascular disease
DCA	Deoxycholic acid
DCs	Dendritic cells
D-PLA	D-phenyllactic acid
FMT	Fecal microbiota transplantation
FMT	Fecal microbiota transplantation
GALT	Gut-associated lymphoid tissues
GF	Germ-free
GFD	Gluten free diet
GI	Gastrointestinal tract
GLP-1	Glucagon-like peptide-1
GPCRs	G-protein-coupled receptors
HCA3	Hydroxycarboxylic acid
HDAC	Histone deacetylase
HDACs	Histone deacetylases
HFD	High-fat diet
IBD	Inflammatory bowel diseases
IECs	Intestinal epithelial cells
ILCs	Innate lymphoid cells
ILFs	Isolated lymphoid follicles
LAB	Lactic acid bacteria
LP	Lamina propria
LPS	Lipopolysaccharide
MACs	Microbiota accessible carbohydrates
MAMPs	Microbe-associated molecular patterns
MDD	Major depressive disorder
Mφ	Macrophages
MTB	Mycobacterium tuberculosis
NADPH	Nicotinamide-adenine dinucleotide phosphate
MAFLD	Metabolic dysfunction-associated fatty liver disease
MASH	Metabolic dysfunction-associated steatohepatitis
NF-kB	Nuclear factor kappa-light-chain-enhancer of activated B cells
NK	Natural killer
PD	Parkinson’s disease
PPs	Peyer’s patches
PRRs	Pattern-recognition receptors
PYY	Plasma peptide YY
RAAS	Renin–angiotensin–aldosterone system
ROS	Reactive oxygen species
SAD	Social anxiety disorder
SCFAs	Short-chain fatty acids
SCN	Suprachiasmatic nucleus
TB	Tuberculosis
TCR	T cell receptor
TLR	Toll-like receptor
TMA	Trimethylamine
TMAO	Trimethylamine-N-oxide
UC	Ulcerative colitis
UPF	Ultra-processed food